LAMMPS (18 Feb 2013)
# Simple rigid body system

units		lj
atom_style	atomic

pair_style	lj/cut 2.5

read_data	data.rigid
  orthogonal box = (-12 -12 -12) to (12 12 12)
  1 by 1 by 1 MPI processor grid
  81 atoms

velocity 	all create 100.0 4928459

# unconnected bodies

#group		clump1 id <> 1 9
#group		clump2 id <> 10 18
#group		clump3 id <> 19 27
#group		clump4 id <> 28 36
#group		clump5 id <> 37 45
#group		clump6 id <> 46 54
#group		clump7 id <> 55 63
#group		clump8 id <> 64 72
#group		clump9 id <> 73 81

#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 #	  	      clump6 clump7 clump8 clump9

# 1 chain of connected bodies

group		clump1 id <> 1 9
9 atoms in group clump1
group		clump2 id <> 9 18
10 atoms in group clump2
group		clump3 id <> 18 27
10 atoms in group clump3
group		clump4 id <> 27 36
10 atoms in group clump4
group		clump5 id <> 36 45
10 atoms in group clump5
group		clump6 id <> 45 54
10 atoms in group clump6
group		clump7 id <> 54 63
10 atoms in group clump7
group		clump8 id <> 63 72
10 atoms in group clump8
group		clump9 id <> 72 81
10 atoms in group clump9

fix 1 all poems group clump1 clump2 clump3 clump4 clump5 	  	      clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms

# 2 chains of connected bodies

#group		clump1 id <> 1 9
#group		clump2 id <> 9 18
#group		clump3 id <> 18 27
#group		clump4 id <> 27 36
#group		clump5 id <> 37 45
#group		clump6 id <> 45 54
#group		clump7 id <> 54 63
#group		clump8 id <> 63 72
#group		clump9 id <> 72 81

#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9

neigh_modify	exclude group clump1 clump1
neigh_modify	exclude group clump2 clump2
neigh_modify	exclude group clump3 clump3
neigh_modify	exclude group clump4 clump4
neigh_modify	exclude group clump5 clump5
neigh_modify	exclude group clump6 clump6
neigh_modify	exclude group clump7 clump7
neigh_modify	exclude group clump8 clump8
neigh_modify	exclude group clump9 clump9

thermo		100

#dump		1 all atom 50 dump.rigid.poems

#dump		1 all image 100 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30
#dump_modify	1 pad 5

timestep 	0.0001
thermo		50
run		10000
Memory usage per processor = 1.94392 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0     217.7783    3430.3907            0    3466.6871   -2.7403788 
      50    13679.637    1404.2468            0    3684.1863    12.446066 
     100    16777.225    888.87665            0    3685.0808   -31.828677 
     150    19595.365    418.45042            0    3684.3446    40.709078 
     200    18524.188    596.47273            0    3683.8375   -0.8159371 
     250    21015.789    180.96521            0    3683.5967   -10.042469 
     300    20785.513    219.25314            0    3683.5053    2.6452719 
     350     21072.46     171.2554            0    3683.3321    7.0609024 
     400    19956.414    356.36381            0    3682.4328    19.320259 
     450     20724.42    227.73284            0    3681.8028    8.1259249 
     500    20152.578    322.71466            0    3681.4777    5.4929878 
     550    20017.022    345.29701            0    3681.4673    5.4661666 
     600    17897.743    698.72196            0    3681.6791    3.2854742 
     650    17297.758    796.60256            0    3679.5623    15.191113 
     700    18581.934    584.29715            0    3681.2861    5.1588289 
     750    21774.158    52.821062            0    3681.8474   -10.775664 
     800    21604.055    81.188546            0    3681.8644   -3.2045743 
     850    17821.483    711.53827            0    3681.7854    7.4384278 
     900    21033.292    175.98127            0    3681.5299   -16.345167 
     950    20968.166    186.59847            0    3681.2929    -2.330456 
    1000     20490.66    266.19375            0    3681.3037    11.787983 
    1050    20222.396    310.94072            0      3681.34   -8.3459539 
    1100    21321.687    127.61533            0    3681.2299   -1.2184717 
    1150    20849.582    206.01695            0    3680.9472  -0.86699139 
    1200    21815.003    45.317413            0    3681.1512    1.5988314 
    1250    18655.437    572.41453            0     3681.654    10.064079 
    1300    20780.781    217.36508            0    3680.8286    6.0538613 
    1350    20558.971    254.36484            0    3680.8601   -3.6773928 
    1400    21485.029    99.812897            0    3680.6511   -16.185475 
    1450    21771.107    52.159622            0    3680.6775   -2.4756668 
    1500    21520.948     93.50391            0    3680.3286    2.1023576 
    1550    21351.418    121.68135            0    3680.2511    5.5159926 
    1600    20778.805    216.92181            0    3680.0559    15.089192 
    1650    21477.637    100.21848            0    3679.8247   -1.1045589 
    1700    18501.336    596.47967            0    3680.0357   -15.679718 
    1750    18563.641    587.34804            0    3681.2882    33.532242 
    1800    19110.182    494.82394            0    3679.8543    18.024056 
    1850    21364.187    119.23612            0    3679.9339    2.5290785 
    1900    20146.615    322.15055            0    3679.9197    5.7314455 
    1950    20692.672    231.25319            0    3680.0319    4.2977815 
    2000    20943.904    189.11228            0    3679.7629     -22.6447 
    2050    19667.984    401.84213            0    3679.8394    3.6248494 
    2100    20280.339    299.77895            0    3679.8354     7.480669 
    2150     19181.64    483.55835            0    3680.4983    22.624694 
    2200    21300.479    130.65196            0    3680.7318    4.7093384 
    2250    20486.287    266.74857            0    3681.1297   -8.6495123 
    2300    18651.575    572.50504            0    3681.1009    -5.261082 
    2350    21514.238    95.495372            0    3681.2017   -9.3698609 
    2400    21465.082    103.76223            0    3681.2758   -29.530492 
    2450    20102.547     331.8625            0    3682.2869    35.630207 
    2500    20766.689    221.28369            0    3682.3986     -12.4229 
    2550    20456.257    272.87511            0    3682.2513   -22.515235 
    2600    21464.354    104.88637            0    3682.2788   -10.110008 
    2650    20885.777    201.39511            0     3682.358    5.0268371 
    2700    18576.387    586.63809            0    3682.7026    22.269183 
    2750    21023.584    178.26789            0    3682.1985   -8.8172166 
    2800    21363.884    121.51908            0    3682.1664    -6.913586 
    2850    17264.155    805.16849            0    3682.5276    29.921611 
    2900    19751.146    390.19286            0    3682.0506    8.8575471 
    2950    21171.167    153.48579            0    3682.0136    1.9171651 
    3000    18698.646     565.2524            0    3681.6934   -16.611709 
    3050    19756.096    389.49951            0    3682.1822   0.79771573 
    3100    20716.934    229.53125            0    3682.3536    18.675629 
    3150    21107.033    164.26375            0    3682.1026     6.292817 
    3200    21194.557    149.62327            0    3682.0495   0.40762301 
    3250    19019.061    511.83944            0     3681.683   -1.0191767 
    3300    19904.232    364.91979            0    3682.2917     1.580824 
    3350    19383.048    452.00672            0    3682.5146    8.9939778 
    3400    18629.871    577.12591            0    3682.1044    19.393397 
    3450    20366.419    287.55662            0    3681.9598    6.7676479 
    3500    20957.937    189.21014            0    3682.1996      9.17515 
    3550    21807.252    47.635006            0    3682.1771    2.2490841 
    3600    21690.617    67.029898            0    3682.1327   -1.4725416 
    3650    21600.202    82.085085            0    3682.1188   -3.9470263 
    3700    19902.074    365.09934            0    3682.1117    3.5789954 
    3750    20669.825    237.14074            0    3682.1116    -7.992071 
    3800    20226.287    311.40404            0    3682.4519   -11.829103 
    3850    20713.814    230.18758            0    3682.4899    -11.37713 
    3900    19621.738    411.85323            0    3682.1428  -0.86016858 
    3950    20828.921    210.87742            0    3682.3643   -1.7978283 
    4000    21734.525    60.230547            0    3682.6513    3.0013342 
    4050    19859.621     371.8688            0    3681.8056     19.53421 
    4100    20748.845    224.82927            0    3682.9701  -0.67873587 
    4150    19578.269    420.02964            0    3683.0745     4.448634 
    4200    19142.314    492.92862            0    3683.3143    7.5300212 
    4250    20189.963    318.02141            0    3683.0152    2.2489634 
    4300    20569.793     254.7842            0    3683.0831     2.014004 
    4350    21505.248    99.029749            0    3683.2377   -1.8448103 
    4400    21795.012    50.799563            0    3683.3016   -3.3446933 
    4450    21630.638     78.27653            0    3683.3829   0.97935456 
    4500    20485.622    268.77758            0    3683.0479    9.0931688 
    4550    21328.202    128.77982            0    3683.4802    6.9392514 
    4600    20425.456     279.4671            0    3683.7097    14.657178 
    4650    21734.316    61.575892            0    3683.9619   -6.1228621 
    4700    20377.517    287.77871            0    3684.0315   -10.350636 
    4750    21765.762    56.481378            0    3684.1084   -13.686961 
    4800    21064.967    173.07588            0    3683.9038   -3.5246286 
    4850    21496.739    100.96272            0    3683.7525    3.4134893 
    4900    21387.734    118.85944            0    3683.4818    2.7545377 
    4950    21606.598    82.305575            0    3683.4052    2.7661083 
    5000    20813.389    211.50552            0    3680.4037     -1.99709 
    5050    21258.837     140.0257            0    3683.1652   -4.6011608 
    5100      18840.1    543.32464            0    3683.3413    31.178048 
    5150    22005.655    16.168882            0     3683.778   -4.3729594 
    5200    20808.086    215.87951            0    3683.8939    7.4410336 
    5250    18679.669    570.83153            0    3684.1098    14.191478 
    5300    19753.173    391.94671            0    3684.1422   -8.5241508 
    5350    21608.313    82.705694            0    3684.0912   -3.6094817 
    5400    21488.174    102.68409            0    3684.0464    4.2600964 
    5450    17518.356    764.26875            0    3683.9947  -0.12243804 
    5500    21696.071    68.069788            0    3684.0816   -1.5476526 
    5550    18502.148     599.7684            0    3683.4597    37.379976 
    5600    18128.267    662.17376            0    3683.5516    16.554047 
    5650     18537.13     594.3189            0    3683.8406     12.05774 
    5700    20851.723    208.91824            0    3684.2053   -4.3830301 
    5750    20941.372    194.08984            0    3684.3185   -0.1943864 
    5800    20194.472    318.72727            0    3684.4726     5.154744 
    5850    20856.188    208.56814            0    3684.5994    3.2314482 
    5900    21125.245    164.07233            0    3684.9465  -0.33002911 
    5950    20138.458    328.54345            0    3684.9532    10.557313 
    6000    20981.486    188.51066            0    3685.4249   -9.0163197 
    6050    20822.112    215.14903            0    3685.5011   -18.139995 
    6100    20076.859    339.70008            0    3685.8432   -3.0307257 
    6150    19953.615    360.46342            0     3686.066    8.3344429 
    6200    20903.384    202.40101            0    3686.2984  -0.39424049 
    6250    21134.826    163.89116            0    3686.3621   -4.1668704 
    6300    21258.213    143.90658            0    3686.9422    -7.391516 
    6350    20373.797    291.10416            0    3686.7369   -14.895748 
    6400    19051.752     510.8571            0    3686.1491 -0.078518196 
    6450     19649.32    412.61991            0    3687.5065   -1.5921483 
    6500    20142.923    330.66911            0    3687.8229    6.8022912 
    6550    19574.327    424.60137            0    3686.9891     11.82743 
    6600    16105.355    1002.7817            0    3687.0076    17.558797 
    6650    21537.744    97.953562            0    3687.5775     2.735191 
    6700    16808.381    887.46461            0    3688.8614   -9.3638392 
    6750    16391.199    958.16942            0    3690.0359    24.040757 
    6800     19891.18    371.95843            0    3687.1551   -25.326616 
    6850    19344.505    464.12314            0    3688.2073    -16.88882 
    6900    21489.989    106.09106            0    3687.7559   -2.7741331 
    6950    19023.694    517.19865            0    3687.8143    12.795625 
    7000    21072.663    175.47912            0    3687.5897   -4.6260178 
    7050    19697.946    404.85665            0    3687.8476   0.96426982 
    7100    20684.854    240.16243            0     3687.638   -6.9283531 
    7150    20888.947    205.87412            0    3687.3653    2.4592293 
    7200    20709.233    235.52341            0    3687.0622    1.8850608 
    7250    20644.676    246.05983            0    3686.8391   -1.9432958 
    7300    19940.501    363.58269            0    3686.9996    8.7916219 
    7350    20904.854    202.70884            0    3686.8511    1.1932912 
    7400    19794.615    388.44762            0    3687.5502    4.2494869 
    7450    20398.713    287.96541            0    3687.7509    1.9565661 
    7500    14969.907    1195.4664            0     3690.451     61.49775 
    7550    20048.243    346.41733            0    3687.7911    8.8637262 
    7600    13724.843    1400.6649            0    3688.1386   -28.102927 
    7650    17323.581    800.37606            0    3687.6396    17.015401 
    7700    20781.624     224.2726            0    3687.8767    2.5260419 
    7750     19629.33    416.31516            0    3687.8702     18.39744 
    7800    20804.173    220.99571            0    3688.3579    11.409891 
    7850    20756.856    228.60421            0    3688.0803    -33.84006 
    7900    21716.444    68.965593            0    3688.3729   -12.291272 
    7950    19610.154    419.14133            0    3687.5002    1.7759679 
    8000    18622.409    585.42868            0    3689.1635    26.686729 
    8050    19777.369    392.63726            0    3688.8654   -22.209128 
    8100    16497.521    939.24542            0    3688.8322   -42.367659 
    8150     19446.13     444.3108            0    3685.3324    32.613169 
    8200    20411.209     286.5915            0    3688.4597   -5.2887315 
    8250    14328.544    1302.6847            0    3690.7753    15.143982 
    8300    21405.234    121.47682            0    3689.0157   -4.6378296 
    8350    15481.055    1109.2428            0    3689.4186     57.85088 
    8400    14139.682     1332.356            0    3688.9697   -0.1974486 
    8450    15623.736    1084.5594            0    3688.5155    37.668188 
    8500    18872.571    543.29677            0    3688.7253   -11.622477 
    8550    18568.346    594.15647            0    3688.8809  -0.53198127 
    8600    18857.924    546.26599            0    3689.2533    6.9976522 
    8650    20422.926    285.18311            0    3689.0041   -2.1124395 
    8700    15904.428    1038.6394            0    3689.3774    11.108432 
    8750    17585.096    758.32272            0     3689.172   -13.175342 
    8800    19561.883     429.1997            0    3689.5135    31.379344 
    8850    21083.378    174.46783            0    3688.3642    -1.405537 
    8900    21922.179    35.258703            0    3688.9551   0.92994553 
    8950    15270.836    1145.5748            0     3690.714     59.72214 
    9000     21236.73    149.52929            0    3688.9843    3.6894217 
    9050    20391.028    289.54828            0     3688.053   -12.318301 
    9100      19963.6    361.58733            0     3688.854   -1.6201635 
    9150      20852.5    213.26173            0    3688.6783    3.4781812 
    9200    17559.276    763.58389            0      3690.13    23.653055 
    9250    20719.763    235.38861            0    3688.6825   -7.2385902 
    9300    20210.461    320.16875            0    3688.5789   0.71513298 
    9350    20589.665    256.39159            0    3688.0025    11.766742 
    9400    21888.845    39.743204            0     3687.884    0.2325157 
    9450    19995.034    355.22797            0    3687.7336   -30.801824 
    9500    20562.534    260.81379            0    3687.9028    7.6818244 
    9550    20724.259    233.42976            0    3687.4729    2.5906906 
    9600    21156.272    161.92778            0    3687.9731   -3.6794578 
    9650    15407.774    1117.1504            0    3685.1127    10.296536 
    9700    20086.616    339.94203            0    3687.7114      6.85039 
    9750    21017.639    184.92766            0    3687.8675    -4.924906 
    9800    17788.545    723.17057            0     3687.928    19.866063 
    9850    21918.073    35.503859            0     3688.516   -1.9119993 
    9900    17765.237    727.83046            0    3688.7033    19.055502 
    9950    21306.635    137.72864            0    3688.8345   -5.5977574 
   10000    21575.787    92.853786            0    3688.8182   -4.0094168 
Loop time of 3.46636 on 1 procs for 10000 steps with 81 atoms

Pair  time (%) = 0.153362 (4.42429)
Neigh time (%) = 0.0939829 (2.71129)
Comm  time (%) = 0.0105836 (0.305325)
Outpt time (%) = 0.00204635 (0.0590345)
Other time (%) = 3.20638 (92.5001)

Nlocal:    81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    56 ave 56 max 56 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    750 ave 750 max 750 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 750
Ave neighs/atom = 9.25926
Neighbor list builds = 990
Dangerous builds = 927
